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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttctttttttctaactttgtagatcattttttgtttcttatttaagtaatgttggttaactgaaataaggtattgattattcccttatgttttgctagAGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC

Basic information

species Zea mays
transcript GRMZM2G156638_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156638_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g51370.2 (Oryza sativa), 3'ss of exon 7
gttttctttttttctaactttgtaga--tcattttttgttt-cttatttaagtaatgttggttaactgaaa-taaggtattgattattcccttatgttttgctagAGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC
   || | ||| |  ||||| | | |  |||||| |    | ||||||||| |||| |  ||||| ||| | |  |   |  ||| || ||||   ||||||||||||||||||||||| |||||||| ||| |||||||||||||
--gttttctttctggaacttagcacacttcatttctaaaatgcttatttaa-taatatcagttaattgagagtctgacttcaattctttccttcctttttgctagAGCCGCTATTACAGATCTCCAGAAGTTATCCTTGGCTATCC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211005146|gb|FL015709.1|FL015709
EST:     ATTTTGGATCAGCCTGCCTGGAGGGTAAAACGGTTTACTCGTACATCCAG                         AGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC
genomic: ATTTTGGATCAGCCTGCCTGGAGGGTAAAACGGTTTACTCGTACATCCAGgttttctttt ... gttttgctagAGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC
EST: gi|71437996|gb|DR819046.1|DR819046
EST:     ATTTTGGATCAGCCTGCCTGGAGGGTAAAACGGTTTACTCGTACATCCAG                         AGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC
genomic: ATTTTGGATCAGCCTGCCTGGAGGGTAAAACGGTTTACTCGTACATCCAGgttttctttt ... gttttgctagAGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 271

TGTCACAACAGCTGCAGAAGTGAAAGTTATTGATTTTGGATCAGCCTGCCTGGAGGGTAAAACGGTTTACTCGTACATCCAGgttttctttt ... gttttgctagAGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 339

TGTCACAACAGCTGCAGAAGTGAAAGTTATTGATTTTGGATCAGCCTGCCTGGAGGGTAAAACGGTTTACTCGTACATCCAGgttttctttt ... gttttgctagAGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 258

TGTCACAACAGCTGCAGAAGTGAAAGTTATTGATTTTGGATCAGCCTGCCTGGAGGGTAAAACGGTTTACTCGTACATCCAGgttttctttt ... gttttgctagAGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 298

TGTCACAACAGCTGCAGAAGTGAAAGTTATTGATTTTGGATCAGCCTGCCTGGAGGGTAAAACGGTTTACTCGTACATCCAGgttttctttt ... gttttgctagAGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtaatgttggttaactgaaataaggtattgattattcccttatgttttgctagAGCCGCTATTACAGGTCTCCAGAGGTTCTCCTTGGCTATCC
                           tattgat  putative branch site (score: 298)
                                    ttcccttatgtttt  putative PPT
                           tattgattatt  TA-rich tract